org.sbml.libsbml

Class Output

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.Output

public class Output
extends SBase

qual The Output class for the Qualitative Models package.

Each Output refers to a QualitativeSpecies that participates in (is affected by) the corresponding Transition. In Petri net models these are the output places of the transition.

In a logical model, a QualitativeSpecies should be referenced in at most one ListOfOutputs, (that of the Transition defining the evolution of this species). When a Transition has several outputs, it is because the referenced species share the same regulators and the same logical rules.

Constructor Summary

Constructors

Constructor and Description
Output() Creates a new Output with the given level, version, and package version.
Output(long level) Creates a new Output with the given level, version, and package version.
Output(long level, long version) Creates a new Output with the given level, version, and package version.
Output(long level, long version, long pkgVersion) Creates a new Output with the given level, version, and package version.
Output(Output orig) Copy constructor for Output.
Output(QualPkgNamespaces qualns) Creates a new Output with the given QualPkgNamespaces object.

Method Summary

Methods

Modifier and Type	Method and Description
Output	cloneObject() Creates and returns a deep copy of this Output object.
void	delete() Explicitly deletes the underlying native object.
java.lang.String	getElementName() Returns the XML element name of this object, which for Output, is always 'output'.
java.lang.String	getId() Returns the value of the 'id' attribute of this Output.
java.lang.String	getName() Returns the value of the 'name' attribute of this Output.
int	getOutputLevel() Returns the value of the 'outputLevel' attribute of this Output.
java.lang.String	getQualitativeSpecies() Returns the value of the 'qualitativeSpecies' attribute of this Output.
int	getTransitionEffect() Returns the value of the 'transitionEffect' attribute of this Output.
int	getTypeCode() Returns the libSBML type code of this object instance.
boolean	hasRequiredAttributes() Predicate returning true if all the required attributes for this Output object have been set.
boolean	isSetId() Predicate returning true or false depending on whether this Output's 'id' attribute has been set.
boolean	isSetName() Predicate returning true or false depending on whether this Output's 'name' attribute has been set.
boolean	isSetOutputLevel() Predicate returning true or false depending on whether this Output's 'outputLevel' attribute has been set.
boolean	isSetQualitativeSpecies() Predicate returning true or false depending on whether this Output's 'qualitativeSpecies' attribute has been set.
boolean	isSetTransitionEffect() Predicate returning true or false depending on whether this Output's 'transitionEffect' attribute has been set.
void	renameSIdRefs(java.lang.String oldid, java.lang.String newid) Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
int	setId(java.lang.String id) Sets the value of the 'id' attribute of this Output.
int	setName(java.lang.String name) Sets the value of the 'name' attribute of this Output.
int	setOutputLevel(int outputLevel) Sets the value of the 'outputLevel' attribute of this Output.
int	setQualitativeSpecies(java.lang.String qualitativeSpecies) Sets the value of the 'qualitativeSpecies' attribute of this Output.
int	setTransitionEffect(int transitionEffect) Sets the value of the 'transitionEffect' attribute of this Output.
int	unsetId() Unsets the value of the 'id' attribute of this Output.
int	unsetName() Unsets the value of the 'name' attribute of this Output.
int	unsetOutputLevel() Unsets the value of the 'outputLevel' attribute of this Output.
int	unsetQualitativeSpecies() Unsets the value of the 'qualitativeSpecies' attribute of this Output.
int	unsetTransitionEffect() Unsets the value of the 'transitionEffect' attribute of this Output.

Methods inherited from class org.sbml.libsbml.SBase

addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Output

public Output()
       throws SBMLConstructorException

Creates a new Output with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this Output

version - a long integer, the SBML Version to assign to this Output

pkgVersion - a long integer, the SBML Qual Version to assign to this Output

Throws:

SBMLConstructorException

Output

public Output(long level)
       throws SBMLConstructorException

Creates a new Output with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this Output

version - a long integer, the SBML Version to assign to this Output

pkgVersion - a long integer, the SBML Qual Version to assign to this Output

Throws:

SBMLConstructorException

Output

public Output(long level,
      long version)
       throws SBMLConstructorException

Creates a new Output with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this Output

version - a long integer, the SBML Version to assign to this Output

pkgVersion - a long integer, the SBML Qual Version to assign to this Output

Throws:

SBMLConstructorException

Output

public Output(long level,
      long version,
      long pkgVersion)
       throws SBMLConstructorException

Creates a new Output with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this Output

version - a long integer, the SBML Version to assign to this Output

pkgVersion - a long integer, the SBML Qual Version to assign to this Output

Throws:

SBMLConstructorException

Output

public Output(Output orig)
       throws SBMLConstructorException

Copy constructor for Output.

Parameters:

orig - the Output instance to copy.

Throws:

SBMLConstructorException

Output

public Output(QualPkgNamespaces qualns)
       throws SBMLConstructorException

Creates a new Output with the given QualPkgNamespaces object.

Parameters:

qualns - the QualPkgNamespaces object

Throws:

SBMLConstructorException

Method Detail

cloneObject

public Output cloneObject()

Creates and returns a deep copy of this Output object.

Overrides:

cloneObject in class SBase

Returns:

a (deep) copy of this Output object.

delete

public void delete()

Explicitly deletes the underlying native object.

In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the Output.delete() method on the libSBML object.

This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke Output.delete() themselves.

Overrides:

delete in class SBase

getElementName

public java.lang.String getElementName()

Returns the XML element name of this object, which for Output, is always 'output'.

Overrides:

getElementName in class SBase

Returns:

the name of this element, i.e. 'output'.

getId

public java.lang.String getId()

Returns the value of the 'id' attribute of this Output.

Overrides:

getId in class SBase

Returns:

the value of the 'id' attribute of this Output as a string.

getName

public java.lang.String getName()

Returns the value of the 'name' attribute of this Output.

Overrides:

getName in class SBase

Returns:

the value of the 'name' attribute of this Output as a string.

getOutputLevel

public int getOutputLevel()

Returns the value of the 'outputLevel' attribute of this Output.

Returns:

the value of the 'outputLevel' attribute of this Output as a integer.

getQualitativeSpecies

public java.lang.String getQualitativeSpecies()

Returns the value of the 'qualitativeSpecies' attribute of this Output.

Returns:

the value of the 'qualitativeSpecies' attribute of this Output as a string.

getTransitionEffect

public int getTransitionEffect()

Returns the value of the 'transitionEffect' attribute of this Output.

Returns:

the value of the 'transitionEffect' attribute of this Output as a string.

getTypeCode

public int getTypeCode()

Returns the libSBML type code of this object instance.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters &ldquoSBML_&rdquo. In the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. Note that different Level 3 package plug-ins may use overlapping type codes to identify the package to which a given object belongs, call the getPackageName() method on the object.

Overrides:

getTypeCode in class SBase

Returns:

the SBML type code for this object: SBML_QUAL_OUTPUT

See Also:

Output.getElementName(), SBase.getPackageName()

"Warning:"

The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().

hasRequiredAttributes

public boolean hasRequiredAttributes()

Predicate returning true if all the required attributes for this Output object have been set.

Overrides:

hasRequiredAttributes in class SBase

Returns:

a boolean value indicating whether all the required attributes for this object have been defined.

"Note:"

The required attributes for a Output object are:

• 'qualitativeSpecies'
• 'transitionEffect'

isSetId

public boolean isSetId()

Predicate returning true or false depending on whether this Output's 'id' attribute has been set.

Overrides:

isSetId in class SBase

Returns:

true if this Output's 'id' attribute has been set, otherwise false is returned.

isSetName

public boolean isSetName()

Predicate returning true or false depending on whether this Output's 'name' attribute has been set.

Overrides:

isSetName in class SBase

Returns:

true if this Output's 'name' attribute has been set, otherwise false is returned.

isSetOutputLevel

public boolean isSetOutputLevel()

Predicate returning true or false depending on whether this Output's 'outputLevel' attribute has been set.

Returns:

true if this Output's 'outputLevel' attribute has been set, otherwise false is returned.

isSetQualitativeSpecies

public boolean isSetQualitativeSpecies()

Predicate returning true or false depending on whether this Output's 'qualitativeSpecies' attribute has been set.

Returns:

true if this Output's 'qualitativeSpecies' attribute has been set, otherwise false is returned.

isSetTransitionEffect

public boolean isSetTransitionEffect()

Predicate returning true or false depending on whether this Output's 'transitionEffect' attribute has been set.

Returns:

true if this Output's 'transitionEffect' attribute has been set, otherwise false is returned.

renameSIdRefs

public void renameSIdRefs(java.lang.String oldid,
                 java.lang.String newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of @p oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Overrides:

renameSIdRefs in class SBase

Parameters:

oldid - the old identifier

newid - the new identifier

setId

public int setId(java.lang.String id)

Sets the value of the 'id' attribute of this Output.

Overrides:

setId in class SBase

Parameters:

id - String value of the 'id' attribute to be set

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setName

public int setName(java.lang.String name)

Sets the value of the 'name' attribute of this Output.

Overrides:

setName in class SBase

Parameters:

name - String value of the 'name' attribute to be set

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setOutputLevel

public int setOutputLevel(int outputLevel)

Sets the value of the 'outputLevel' attribute of this Output.

Parameters:

outputLevel - int value of the 'outputLevel' attribute to be set

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setQualitativeSpecies

public int setQualitativeSpecies(java.lang.String qualitativeSpecies)

Sets the value of the 'qualitativeSpecies' attribute of this Output.

Parameters:

qualitativeSpecies - String value of the 'qualitativeSpecies' attribute to be set

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

setTransitionEffect

public int setTransitionEffect(int transitionEffect)

Sets the value of the 'transitionEffect' attribute of this Output.

Parameters:

transitionEffect - String value of the 'transitionEffect' attribute to be set

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

unsetId

public int unsetId()

Unsets the value of the 'id' attribute of this Output.

Overrides:

unsetId in class SBase

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

unsetName

public int unsetName()

Unsets the value of the 'name' attribute of this Output.

Overrides:

unsetName in class SBase

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

unsetOutputLevel

public int unsetOutputLevel()

Unsets the value of the 'outputLevel' attribute of this Output.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

unsetQualitativeSpecies

public int unsetQualitativeSpecies()

Unsets the value of the 'qualitativeSpecies' attribute of this Output.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

unsetTransitionEffect

public int unsetTransitionEffect()

Unsets the value of the 'transitionEffect' attribute of this Output.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED